[English] 日本語
Yorodumi
- PDB-7kg9: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kg9
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, H56W mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / DIHYDRODIPICOLINATE SYNTHASE
Function / homology
Function and homology information


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / LYSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSaran, S. / Majdi Yazdi, M. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: Fluorescence-based Assay Development for Screening Novel Inhibitors of Dihydrodipicolinate Synthase from Campylobacter jejuni
Authors: Majdi Yazd, M. / Reddy Annadi, K. / Saran, S. / Bhagwat, A. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionOct 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,28651
Polymers205,4006
Non-polymers3,88645
Water13,763764
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,35511
Polymers68,4672
Non-polymers8889
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-10 kcal/mol
Surface area21300 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,88820
Polymers68,4672
Non-polymers1,42118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-2 kcal/mol
Surface area21740 Å2
MethodPISA
3
D: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,04420
Polymers68,4672
Non-polymers1,57718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-26 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.830, 225.170, 200.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-521-

HOH

21E-496-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4:20 or resid 22:24 or resid...
21(chain B and (resid 4:20 or resid 22:24 or resid...
31(chain C and (resid 4:20 or resid 22:24 or resid...
41(chain D and (resid 4:20 or resid 22:24 or resid...
51(chain E and (resid 4:20 or resid 22:24 or resid...
61(chain F and (resid 4:20 or resid 22:24 or resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 20
121(chain A and (resid 4:20 or resid 22:24 or resid...A22 - 24
131(chain A and (resid 4:20 or resid 22:24 or resid...A26 - 28
141(chain A and (resid 4:20 or resid 22:24 or resid...A30 - 56
151(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 67
161(chain A and (resid 4:20 or resid 22:24 or resid...A69 - 70
171(chain A and (resid 4:20 or resid 22:24 or resid...A72 - 73
181(chain A and (resid 4:20 or resid 22:24 or resid...A75 - 96
191(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 298
1101(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 298
1111(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 298
1121(chain A and (resid 4:20 or resid 22:24 or resid...A188
1131(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 298
1141(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 298
1151(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 298
1161(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 298
1171(chain A and (resid 4:20 or resid 22:24 or resid...A4 - 298
211(chain B and (resid 4:20 or resid 22:24 or resid...B4 - 20
221(chain B and (resid 4:20 or resid 22:24 or resid...B22 - 24
231(chain B and (resid 4:20 or resid 22:24 or resid...B26 - 28
241(chain B and (resid 4:20 or resid 22:24 or resid...B30 - 56
251(chain B and (resid 4:20 or resid 22:24 or resid...B69 - 70
261(chain B and (resid 4:20 or resid 22:24 or resid...B72 - 73
271(chain B and (resid 4:20 or resid 22:24 or resid...B75 - 96
281(chain B and (resid 4:20 or resid 22:24 or resid...B3 - 298
291(chain B and (resid 4:20 or resid 22:24 or resid...B3 - 298
2101(chain B and (resid 4:20 or resid 22:24 or resid...B188
2111(chain B and (resid 4:20 or resid 22:24 or resid...B3 - 298
2121(chain B and (resid 4:20 or resid 22:24 or resid...B3 - 298
2131(chain B and (resid 4:20 or resid 22:24 or resid...B3 - 298
2141(chain B and (resid 4:20 or resid 22:24 or resid...B3 - 298
2151(chain B and (resid 4:20 or resid 22:24 or resid...B3 - 298
2161(chain B and (resid 4:20 or resid 22:24 or resid...B3 - 298
311(chain C and (resid 4:20 or resid 22:24 or resid...C4 - 20
321(chain C and (resid 4:20 or resid 22:24 or resid...C22 - 24
331(chain C and (resid 4:20 or resid 22:24 or resid...C26 - 28
341(chain C and (resid 4:20 or resid 22:24 or resid...C30 - 56
351(chain C and (resid 4:20 or resid 22:24 or resid...C69 - 70
361(chain C and (resid 4:20 or resid 22:24 or resid...C72 - 73
371(chain C and (resid 4:20 or resid 22:24 or resid...C75 - 96
381(chain C and (resid 4:20 or resid 22:24 or resid...C3 - 298
391(chain C and (resid 4:20 or resid 22:24 or resid...C3 - 298
3101(chain C and (resid 4:20 or resid 22:24 or resid...C188
3111(chain C and (resid 4:20 or resid 22:24 or resid...C3 - 298
3121(chain C and (resid 4:20 or resid 22:24 or resid...C3 - 298
3131(chain C and (resid 4:20 or resid 22:24 or resid...C3 - 298
3141(chain C and (resid 4:20 or resid 22:24 or resid...C3 - 298
3151(chain C and (resid 4:20 or resid 22:24 or resid...C3 - 298
3161(chain C and (resid 4:20 or resid 22:24 or resid...C3 - 298
411(chain D and (resid 4:20 or resid 22:24 or resid...D4 - 20
421(chain D and (resid 4:20 or resid 22:24 or resid...D22 - 24
431(chain D and (resid 4:20 or resid 22:24 or resid...D26 - 28
441(chain D and (resid 4:20 or resid 22:24 or resid...D30 - 56
451(chain D and (resid 4:20 or resid 22:24 or resid...D69 - 70
461(chain D and (resid 4:20 or resid 22:24 or resid...D72 - 73
471(chain D and (resid 4:20 or resid 22:24 or resid...D75 - 96
481(chain D and (resid 4:20 or resid 22:24 or resid...D-5 - 298
491(chain D and (resid 4:20 or resid 22:24 or resid...D-5 - 298
4101(chain D and (resid 4:20 or resid 22:24 or resid...D188
4111(chain D and (resid 4:20 or resid 22:24 or resid...D-5 - 298
4121(chain D and (resid 4:20 or resid 22:24 or resid...D-5 - 298
4131(chain D and (resid 4:20 or resid 22:24 or resid...D-5 - 298
4141(chain D and (resid 4:20 or resid 22:24 or resid...D-5 - 298
4151(chain D and (resid 4:20 or resid 22:24 or resid...D-5 - 298
4161(chain D and (resid 4:20 or resid 22:24 or resid...D-5 - 298
511(chain E and (resid 4:20 or resid 22:24 or resid...E4 - 20
521(chain E and (resid 4:20 or resid 22:24 or resid...E22 - 24
531(chain E and (resid 4:20 or resid 22:24 or resid...E26 - 28
541(chain E and (resid 4:20 or resid 22:24 or resid...E30 - 56
551(chain E and (resid 4:20 or resid 22:24 or resid...E69 - 70
561(chain E and (resid 4:20 or resid 22:24 or resid...E72 - 73
571(chain E and (resid 4:20 or resid 22:24 or resid...E75 - 96
581(chain E and (resid 4:20 or resid 22:24 or resid...E3 - 298
591(chain E and (resid 4:20 or resid 22:24 or resid...E3 - 298
5101(chain E and (resid 4:20 or resid 22:24 or resid...E188
5111(chain E and (resid 4:20 or resid 22:24 or resid...E3 - 298
5121(chain E and (resid 4:20 or resid 22:24 or resid...E3 - 298
5131(chain E and (resid 4:20 or resid 22:24 or resid...E3 - 298
5141(chain E and (resid 4:20 or resid 22:24 or resid...E3 - 298
5151(chain E and (resid 4:20 or resid 22:24 or resid...E3 - 298
5161(chain E and (resid 4:20 or resid 22:24 or resid...E3 - 298
611(chain F and (resid 4:20 or resid 22:24 or resid...F4 - 20
621(chain F and (resid 4:20 or resid 22:24 or resid...F22 - 24
631(chain F and (resid 4:20 or resid 22:24 or resid...F26 - 28
641(chain F and (resid 4:20 or resid 22:24 or resid...F69 - 70
651(chain F and (resid 4:20 or resid 22:24 or resid...F2 - 67
661(chain F and (resid 4:20 or resid 22:24 or resid...F72 - 73
671(chain F and (resid 4:20 or resid 22:24 or resid...F2 - 96
681(chain F and (resid 4:20 or resid 22:24 or resid...F99 - 159
691(chain F and (resid 4:20 or resid 22:24 or resid...F0
6101(chain F and (resid 4:20 or resid 22:24 or resid...F233 - 23
6111(chain F and (resid 4:20 or resid 22:24 or resid...F236 - 266
6121(chain F and (resid 4:20 or resid 22:24 or resid...F268 - 279
6131(chain F and (resid 4:20 or resid 22:24 or resid...F293
6141(chain F and (resid 4:20 or resid 22:24 or resid...F293
6151(chain F and (resid 4:20 or resid 22:24 or resid...F295 - 298

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34233.320 Da / Num. of mol.: 6 / Mutation: H56W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: dapA, Cj0806 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

-
Non-polymers , 9 types, 809 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.3 / Details: 0.2 M Magnesium acetate, 14 % PEG8000 (pH 7.3)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 11, 2018
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→49.042 Å / Num. obs: 109047 / % possible obs: 92 % / Redundancy: 15 % / Biso Wilson estimate: 21.99 Å2 / CC1/2: 0.94 / Net I/σ(I): 3.47
Reflection shellResolution: 2.06→2.134 Å / Rmerge(I) obs: 0.8518 / Num. unique obs: 10111 / % possible all: 85.99

-
Processing

Software
NameVersionClassification
PHENIXdev_2398refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 2.06→49.042 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3308 5452 5 %
Rwork0.2749 103583 -
obs0.2777 109035 91.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.13 Å2 / Biso mean: 23.9099 Å2 / Biso min: 9.13 Å2
Refinement stepCycle: final / Resolution: 2.06→49.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13762 0 193 764 14719
Biso mean--29.44 23.08 -
Num. residues----1790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314214
X-RAY DIFFRACTIONf_angle_d0.64719127
X-RAY DIFFRACTIONf_chiral_restr0.0452191
X-RAY DIFFRACTIONf_plane_restr0.0042424
X-RAY DIFFRACTIONf_dihedral_angle_d14.1138652
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7483X-RAY DIFFRACTION7.433TORSIONAL
12B7483X-RAY DIFFRACTION7.433TORSIONAL
13C7483X-RAY DIFFRACTION7.433TORSIONAL
14D7483X-RAY DIFFRACTION7.433TORSIONAL
15E7483X-RAY DIFFRACTION7.433TORSIONAL
16F7483X-RAY DIFFRACTION7.433TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.06-2.08340.461670.3814317685
2.0834-2.10790.46611700.3916322586
2.1079-2.13360.47651690.3912320486
2.1336-2.16060.38231700.3843322687
2.1606-2.18910.41941710.3708325187
2.1891-2.21910.43281710.3676325488
2.2191-2.25080.41651730.3577329688
2.2508-2.28440.40711730.3555327488
2.2844-2.32010.36971730.348329189
2.3201-2.35810.37071780.3626338490
2.3581-2.39870.44921740.3495330990
2.3987-2.44240.46391740.352329589
2.4424-2.48930.381780.3385339390
2.4893-2.54020.39381770.3398336291
2.5402-2.59540.36951790.3377339791
2.5954-2.65580.39541830.3291347992
2.6558-2.72220.36421810.3263344692
2.7222-2.79580.35531810.3247343392
2.7958-2.8780.39851820.3158345493
2.878-2.97090.39751840.3355350194
2.9709-3.07710.37441880.3106356294
3.0771-3.20020.37821870.2815356995
3.2002-3.34590.32191910.2666362896
3.3459-3.52220.32471920.255365197
3.5222-3.74280.29371930.2323365597
3.7428-4.03170.26371970.1996373798
4.0317-4.43720.23441950.1841371498
4.4372-5.07870.22731960.1792371598
5.0787-6.39630.25311980.2152377198
6.3963-9.210.23172070.192393198

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more